pysam.SamtoolsError uses a repr() in its __str__ method,

so I always get an escaped error message in the log file when I except pysam.SamtoolsError as e: logfile.write(str(e))

'samtools returned with error 1: stdout=, stderr=samtools index: failed to create index for "some_broken.bam"\n'

I don't think it's necessary to escape error messages, which makes SamtoolsError behave differently than common python Exceptions.

>>> str(pysam.SamtoolsError("error"))
"'error'"
>>> str(Exception("error"))
'error'